Mercurial > repos > devteam > fastx_trimmer
annotate fastx_trimmer.xml @ 1:0288c4b3a53f
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:51:31 -0500 |
| parents | a7d22d34ec70 |
| children | 97f0b63ae7cf |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
| 6 <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output | |
| 7 #if $input.ext == "fastqsanger": | |
| 8 -Q 33 | |
| 9 #end if | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
|
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0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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13 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" /> |
| 0 | 14 |
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0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
15 <param name="first" size="4" type="integer" value="1"> |
| 0 | 16 <label>First base to keep</label> |
| 17 </param> | |
| 18 | |
|
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0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
19 <param name="last" size="4" type="integer" value="21"> |
| 0 | 20 <label>Last base to keep</label> |
| 21 </param> | |
| 22 </inputs> | |
| 23 | |
| 24 <tests> | |
| 25 <test> | |
| 26 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> | |
|
1
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <param name="input" value="fastx_trimmer1.fasta" /> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
28 <param name="first" value="5"/> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
29 <param name="last" value="36"/> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
30 <output name="output" file="fastx_trimmer1.out" /> |
| 0 | 31 </test> |
| 32 <test> | |
| 33 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> | |
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1
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
34 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
35 <param name="first" value="1"/> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
36 <param name="last" value="27"/> |
|
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
37 <output name="output" file="fastx_trimmer2.out" /> |
| 0 | 38 </test> |
| 39 </tests> | |
| 40 | |
| 41 <outputs> | |
|
1
0288c4b3a53f
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
42 <data format="input" name="output" metadata_source="input" /> |
| 0 | 43 </outputs> |
| 44 <help> | |
| 45 **What it does** | |
| 46 | |
| 47 This tool trims (cut bases from) sequences in a FASTA/Q file. | |
| 48 | |
| 49 -------- | |
| 50 | |
| 51 **Example** | |
| 52 | |
| 53 Input Fasta file (with 36 bases in each sequences):: | |
| 54 | |
| 55 >1-1 | |
| 56 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC | |
| 57 >2-1 | |
| 58 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA | |
| 59 | |
| 60 | |
| 61 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: | |
| 62 | |
| 63 >1-1 | |
| 64 TATGGTCAGAAACCATATGCA | |
| 65 >2-1 | |
| 66 CAGCGAGGCTTTAATGCCATT | |
| 67 | |
| 68 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: | |
| 69 | |
| 70 >1-1 | |
| 71 TCAGA | |
| 72 >2-1 | |
| 73 AGGCT | |
| 74 | |
| 75 ------ | |
| 76 | |
| 77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 78 | |
| 79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 80 | |
| 81 </help> | |
| 82 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | |
| 83 </tool> |